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Hi, thank you for your quick reply! Sorry, my explanations were a bit confusing. While looking at the display in FSLview the brain was displayed in a strange way. The labels (RL, AP and IS) were correctly placed around the brain but the sagittal view was displayed at the bottom left of the window (z), the coronal view at the top right (x) and the axial view at the top left (y). If I use this file to do a registration to a standard space, the registration does not work properly. That is why I thought using fslswapdim on the file I have. I looked at #7 in the FSL FAQ you mentioned. It is not completely clear in my head how I should use fslorient on my data. While looking at the header of my original file that comes out from dcm2nii I have: qform_name Unknown qform_code 0 qto_xyz:1 1.000000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 1.000000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 1.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Scanner Anat sform_code 1 sto_xyz:1 0.000000 0.000000 1.000000 -88.105324 sto_xyz:2 -1.000000 0.000000 0.000000 138.895889 sto_xyz:3 0.000000 1.000000 0.000000 -131.237289 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Inferior-to-Superior sform_zorient Left-to-Right Then, I apply fslswapdim original_file -z -x y new_file If I look at the header info of the new file I have qform_name Scanner Anat qform_code 1 qto_xyz:1 -1.000000 0.000000 -0.000000 86.894676 qto_xyz:2 0.000000 1.000000 -0.000000 -116.104111 qto_xyz:3 0.000000 0.000000 1.000000 -131.237289 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Scanner Anat sform_code 1 sto_xyz:1 -1.000000 0.000000 0.000000 86.894676 sto_xyz:2 0.000000 1.000000 0.000000 -116.104111 sto_xyz:3 0.000000 0.000000 1.000000 -131.237289 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior How should I apply fslorient on my new file to make sure the header info are appropriate? Should I copy the sform of the original file (since the qform is unknown)? If yes, how should I copy it? Thank you! Best, Cécile On Mon, Sep 27, 2010 at 11:13 PM, Michael Harms <[log in to unmask]>wrote: > What do you mean by "not well oriented while looking at them in fslview"? > Is the brain just sideways or upside-down in the display, or are the > orientation labels shown within fslview actually in the wrong position? > > You might want to read #7 in the FSL FAQ, which makes clear that using > fslswapdim in the fashion that you appear to be doing (i.e., without > fslorient) will mess up the orientation if you are starting with a valid > nifti file (i.e., one in the which the R/L, A/P, and S/I labels show up in > the proper locations within fslview). > > Best, > -MH > > > > Hi, > > > > I am using feat to run analyses on fMRI data that were acquired > sagittally > > (anatomical and EPI runs). > > > > Because of the direction of the acquisitions, the nifti files created > from > > the dicom with dcm2nii were not well oriented while looking at them in > > fslview and the registration step did not work properly (everything was > > flipped 180°. The frontal lobe of the example_function was in the > > occipital > > of the standard images etc...). > > > > I then decided to re-orient the nifti files using: > > fslswapdim input.nii.gz -z -x y output.nii.gz > > But in doing this I am afraid it might be problematic for the slice > timing > > correction step. Am I right? How does feat determine the slice order and > > the > > direction of slice acquisition? > > > > So as an other solution I kept the run and anatomical we acquired in the > > "wrong orientation" and created an icbm152 template (using fslswapdim -y > z > > -x) with the same orientation as our acquisitions. This way, the > > registration seems to work properly and I could run a group analysis. > > My only concern is about the coordinates of my images. Does fslswapdim > > affect the coordinates of the volume acquired? Are the coordinates of the > > cluster list still accurate (as I used a template with different > > orientations)? > > If I reorient my final group statistic maps in the "right" orientation > > using > > once again fslswapdim (-z -x y), can I use the Atlas tools without having > > to > > worry about the coordinates? > > > > I went through a lot of anterior posts in the FSL archives. That is how I > > discovered fslswapdim (thank you for those very useful posts!). I did not > > find any post regarding analysis of data acquired sagittally though > (maybe > > I > > did not use the right keywords...). > > Any help and suggestions will be very welcome. > > > > Thanks in advance! > > Best, > > > > Cécile Madjar > > >